testtrios.R
In networkR: Network Analysis and Visualization

context("trios - functions for handling id, fid, mid trio information")

## Check output is correct and has not changed
test_that("identify family clusters", {
    id <- 1:11
    fid <- c(NA, NA, 1, 1, NA, 23, 45, 5, 5, 7, NA)
    mid <- c(NA, NA, 2, 2, 65, NA, 46, 6, 6, 6, 0)
    res <- make_family_id(id, fid, mid)
    
    expect_is(res, "integer")
    expect_equal(length(res), length(id))
    expect_equal(res, c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L))

    id <- 1:4
    fid <- c(0, 0, 1, 1)
    mid <- c(0, 0, 2, 2)
    expect_equal(make_family_id(id, fid, mid), c(1L, 1L, 1L, 1L))

    expect_equal(make_family_id(c(1,2), c(3,3), c(4,4)), c(1L, 1L))
})


test_that("identify parental chains", {
    id <- 1:11
    fid <- c(0,0,1,0,0,4,0,0,3,7,7)
    mid <- c(0,0,2,0,0,5,0,0,6,6,8)    
    res <- make_parental_chain(id, fid, mid)
    
    expect_is(res, "integer")
    expect_equal(length(res), length(id))
    expect_equal(res, c(1L, 1L, 2L, 3L, 3L, 2L, 2L, 2L, 4L, 5L, 6L))

})


test_that("trios - consistency", {
    id <- 1:11
    fid <- c(NA, NA, 1, 1, NA, 23, 45, 5, 5, 7, NA)
    mid <- c(NA, NA, 2, 2, 65, NA, 46, 6, 6, 6, 0)

    expect_error(validate_trio_consistency(id, fid, mid), "some individuals")

    id <- 1:12
    fid <- c(NA,  0, 1, 1, NA, 23, 45, 5, 5, 7, 10, 10)
    mid <- c(NA, NA, 2, 2,  0, 56, 46, 6, 6, 6, 9, 11)
    sex <- c( 1,  2, 1, 2,  1,  2, 1, 2, 1, 2, 1, 2)

    expect_equal(validate_trio_consistency(id, fid, mid), TRUE)

    expect_error(validate_trio_consistency(id, fid, mid, sex), "some individuals")

    sex <- c( 1,  2, 1, 2,  1,  2, 1, 2, 2, 1, 2, 2)

    expect_equal(validate_trio_consistency(id, fid, mid, sex), TRUE)
})